3KW3

Crystal structure of alanine racemase from Bartonella henselae with covalently bound pyridoxal phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DY3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8289Native crystal grown in 0.1 M Hepes pH 8.0, 33% PEG 3350 at 42.3 mg/mL, crystal tracking ID 203636d11; crystal used for combined Phaser MR/IodoSAD grown in 0.1 M Hepes pH 8.5, 0.2 M MgCl2, 25% PEG 3350 and soaked for 1 hour in 0.1 M Hepes pH 8.0, 1.0 M KI, 35% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2244.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.794α = 90
b = 54.316β = 112.39
c = 107.476γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-07-11MSINGLE WAVELENGTH
21x-ray100CCDRIGAKU SATURN 944+2009-11-16MSINGLE WAVELENGTH
1,21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.976484ALS5.0.3
2ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1,22.045099.50.08817.45.345971
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,22.042.1296.70.4962.794.64405

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSAD, MRTHROUGHOUT2DY32.0434.945875231898.540.1930.1910.233RANDOM22.817
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.82-1.88-1.010.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.335
r_dihedral_angle_4_deg16.392
r_dihedral_angle_3_deg15.135
r_dihedral_angle_1_deg6.391
r_scangle_it3.061
r_scbond_it1.954
r_angle_refined_deg1.408
r_mcangle_it1.167
r_mcbond_it0.664
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.335
r_dihedral_angle_4_deg16.392
r_dihedral_angle_3_deg15.135
r_dihedral_angle_1_deg6.391
r_scangle_it3.061
r_scbond_it1.954
r_angle_refined_deg1.408
r_mcangle_it1.167
r_mcbond_it0.664
r_chiral_restr0.088
r_bond_refined_d0.014
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5407
Nucleic Acid Atoms
Solvent Atoms426
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
SHELXphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing